|
| Status |
Public on May 23, 2011 |
| Title |
preformed leaf sample from September 2005, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
preformed leaves of Populus deltoides sampled in September 2005
|
| Organism |
Populus deltoides |
| Characteristics |
tissue: preformed leaf tissue
developmental stage: sexually mature tree
collection date: September of 2005
block: 1
|
| Treatment protocol |
NA, sampels represent wild-type tissues
|
| Growth protocol |
Samples were collected from a 30-year old Populus deltoides tree growing next to a stream. Samples were taken for all months except for March at the end of the second week of the month. March samples were collected prior to the terminal bud opening, approximately in the third week of the month.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with a hot-borate method (Wan and Wilkins; 1994) followed by a Dnase I digestion and clean-up using Rneasy Mini Kit (Quigen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using Genechip Scanner 3000 (Affymetrix).
|
| Description |
Gene expression of preformed leaf tissue
|
| Data processing |
Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages. Additionally, the block effect as estimated by the limma model was removed from the GCRMA values.
|
| |
|
| Submission date |
Sep 24, 2010 |
| Last update date |
May 26, 2011 |
| Contact name |
Joshua Adams |
| E-mail(s) |
[email protected]
|
| Phone |
8704601348
|
| Organization name |
University of Arkansas-Monticello
|
| Department |
Forest Resources
|
| Street address |
PO Box 3468
|
| City |
Monticello |
| State/province |
AR |
| ZIP/Postal code |
71656 |
| Country |
USA |
| |
|
| Platform ID |
GPL4359 |
| Series (1) |
| GSE24349 |
Time-course leaf expression data from Populus deltoides |
|
